Unfortunately, Lynn found it difficult to duplicate the extraordinary success of his first season, and was hampered by injuries. These sometimes were caused by fearless play, such as a broken rib caused by crashing into an outfield wall, or knee injuries from breaking up double plays, but most were simply of the nagging variety, such as strains and sprains. Although he didn't maintain the same level of his rookie season, he still excelled, winning three more Gold Gloves in 1978-80 and finishing 4th in the 1979 MVP voting, while being elected to the All-Star team every year with the Red Sox.

Because Lynn longed to play in California, where he had grown up, the Red Sox traded him along with Rick Burleson to the Angels after the 1980 season. However, away from Fenway Park, which was batting average-friendly to left-handed hitters like him, he never hit over .300 again. Lynn did go on to hit more than 20 home runs in six consecutive seasons starting in 1982, and was selected MVP of the 1982 American League Championship Series, the first player from the losing team ever selected. In 1983, he hit the only grand slam in All-Star history and was named MVP after being elected to the team for the ninth consecutive year. His four home runs in All-Star games is second only to Stan Musial.

In 1981, at a point in his career when it looked like he would one day rank among the game's all-time greats, Lawrence Ritter and Donald Honig included him in their book The 100 Greatest Baseball Players of All Time.

Following the 1984 season, Lynn signed a lucrative contract with the Orioles, who signed numerous free agents in the mid-1980s in an ultimately unsuccessful effort to win another World Series after their 1983 title. At this time, one newspaper report criticized Lynn saying, "He could pull a hamstring while taking a shower." Lynn never played more than 150 games in a season and only topped 140 games four times. From 1982-1988, his home run totals were 21-22-23-23-23-23-25. His 4 consecutive years of exactly 23 home runs tied Ken Boyer (24 each year for Cardinals from 1961-1964) for most consecutive years with exactly the same number of home runs (based on 20 or more home runs).

Detroit acquired Lynn for their 1988 pennant drive, which also proved unsuccessful. There was some initial controversy with this trade, because even though the trade itself was made on the day of the trading deadline, while Lynn was en route to Detroit, he was technically not in "Detroit airspace" when the deadline passed, so he was ruled ineligible for the postseason. MLB Commissioner Fay Vincent later overruled this decision, declaring that as long as the transaction was completed by the deadline, the player need not physically be in the new team's city to be eligible to play in the playoffs. The point became moot when Detroit failed to qualify for the playoffs that year. For the first time, he was playing in a park which favored left-handed power hitters, but age and injuries had taken their toll. Following a disappointing 1989 season, Lynn wrapped up his career with one season with San Diego in 1990, retiring at the age of 38 with career statistics which, while outstanding, only hinted at his early potential.